Building and analyzing residue interaction networks with cofactors (includes tutorial).

Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and ML/AI.

Order parameter calculations from Desmond Maestro .csv out files

A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

Molecular Dynamics Trajectory Analysis Tools

A package to find collective variables of dynamical systems by training neural networks

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan

A package for multiple-scale simulations on the dynamical and kinetic processes in materials

Gromacs Analysis Library for Rust

Library for Reading Gromacs TPR Files

Repository for my senior design project/thesis code

A Python module for performing data analysis of atomistic trajectories relevant for glasses and supercooled liquids.

"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC

Calculate lipid order parameters from Gromacs simulations

A python molecular dynamics data analysis tool.

A user-friendly Python package to manipulate input and output files of LAMMPS molecular dynamics code. One Python class per LAMMPS file type. Include conversion into pandas DataFrame.

Reactive molecular dynamics trajectory analysis